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Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice

Abstract

The advent of genetically encoded calcium indicators, along with surgical preparations such as thinned skulls or refractive-index-matched skulls, has enabled mesoscale cortical activity imaging in head-fixed mice. However, neural activity during unrestrained behavior substantially differs from neural activity in head-fixed animals. For whole-cortex imaging in freely behaving mice, we present the ‘mini-mScope’, a widefield, miniaturized, head-mounted fluorescence microscope that is compatible with transparent polymer skull preparations. With a field of view of 8 × 10 mm2 and weighing less than 4 g, the mini-mScope can image most of the mouse dorsal cortex with resolutions ranging from 39 to 56 µm. We used the mini-mScope to record mesoscale calcium activity across the dorsal cortex during sensory-evoked stimuli, open field behaviors, social interactions and transitions from wakefulness to sleep.

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Fig. 1: The mini-mScope: a miniaturized head-mounted microscope for whole-cortex mesoscale activity mapping in freely behaving mice.
Fig. 2: Comparison of calcium dynamics imaged with the mini-mScope to conventional widefield epifluorescence macroscope.
Fig. 3: Sensory stimulus-evoked responses imaged by the mini-mScope.
Fig. 4: Mesoscale imaging of the cortex during free and social behavior.
Fig. 5: Combined electrophysiological recording and mesoscale imaging of brain activity during wakefulness and sleep.

Data availability

Data containing videos, pseudocolor maps and images are available upon request from the authors due to the large file sizes. The Allen Brain Atlas was used as an anatomical reference for data analysis in this study (http://www.brain-map.org). All CAD files for manufacturing the mini-mScope are available with this article as Supplementary Data 2. Source data are provided with this paper.

Code availability

All custom code is available on Github at https://github.com/bsbrl/mini-mScope.

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Acknowledgements

S.B.K. acknowledges funds from the Mechanical Engineering Department, College of Science and Engineering, MnDRIVE RSAM initiative of the University of Minnesota, Minnesota Department of Higher Education and National Institutes of Health grant nos. 1R21NS103098-01, 1R01NS111028, 1R21NS112886, RF1NS113287 and 1R21NS111196. L.G. was supported by the University of Minnesota Informatics Institute graduate fellowship. D.A.S. was supported by the University of Minnesota Diversity of Views and Experiences fellowship. M.L.R. was supported by grant no. 1R21NS103098-01-01S1. M.H.M. acknowledges funding from Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant #40352.

Author information

Affiliations

Authors

Contributions

M.L.R., L.G., M.L., D.A.S., L.G., G.W.J. and S.B.K. designed and engineered the mini-mScope. M.L.R., D.A.S., J.D., Z.S.N., O.H., L.G. and S.B.K. designed and executed the experiments. M.L.R., D.A.S., S.L., O.H., V.R. and S.B.K. analyzed the data. M.L.R., D.A.S., S.L., V.R., J.D., M.L. and S.B.K. wrote the manuscript. M.N. and M.H.M. designed and executed the glutamate imaging experiments, analyzed the data and assisted with manuscript writing.

Corresponding author

Correspondence to Suhasa B. Kodandaramaiah.

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Competing interests

The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–8 and Notes 1–7.

Reporting Summary

Supplementary Data 1

Source data for supplementary figures.

Supplementary Video 1

Open field behavior of mouse bearing the mini-mScope. Video depicting a mouse bearing a mini-mScope behaving freely in an open field arena. The mouse is free and comfortable to move throughout the entire arena and rear against the arena walls. The mouse appears undeterred by the mini-mScope or its associated wiring.

Supplementary Video 2

Stability of mesoscale imaging using the mini-mScope during freely moving behavior. Video with top view of mouse moving around in the open field. Epochs of 5–10 s of different behaviors are shown (locomotion, grooming and rearing). Inset: Motion-corrected video of the corresponding cortical calcium dynamics as captured by the mini-mScope.

Supplementary Video 3

Mesoscale calcium dynamics during social behavior. Video with top view of two mice moving around in the open field. Epochs of 10–15 s of different behaviors are shown (no contact and contact). Inset: Motion-corrected video of the corresponding cortical calcium dynamics as captured by the mini-mScope.

Supplementary Data 2

ZIP file containing three main elements. The first is a folder containing the CAD design files. The second is a folder containing the PCB design files. The third is an Excel sheet (Supplementary_File_1.xlsx) containing a master parts list.

Source data

Source Data Fig. 1

Mini-mScope resolution and illumination testing data.

Source Data Fig. 2

Data used to compare the calcium dynamics imaged with the mini-mScope to a conventional widefield epifluorescence macroscope.

Source Data Fig. 3

Data for the sensory stimulus-evoked responses imaged by the mini-mScope.

Source Data Fig. 4

Data for the mesoscale imaging of the cortex during free behavior taken with the mini-mScope.

Source Data Fig. 5

Data for the combined electrophysiological recording and mesoscale imaging of brain activity during sleep recorded with the mini-mScope.

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Rynes, M.L., Surinach, D.A., Linn, S. et al. Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice. Nat Methods 18, 417–425 (2021). https://doi.org/10.1038/s41592-021-01104-8

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